Mixed-Effects Models in S and S-Plus

By V. Carey, You-Gan Wang. 2001

7,766 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/57feb4bf13196495799e65e8cf348ece5c913306

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In Statistics and Probability

Citations in the corpus

Global warming benefits the small in aquatic ecosystems (2009, methodology): “For experimental data, we used LME models (41) to evaluate the effect of temperature on the dependent variables (see Fig.”
A statistical framework to explore ontogenetic growth variation among individuals and populations: a marine fish example (2015, methodology): “Compound symmetry does have applicability in models with short time series per group (as is generally the case here for each fish; Pinheiro and Bates 2000:228), although perhaps a more appropriate method (not available in lme4) would be an autoregressive process (e.g., AR-1).”
MAXIMUM LIKELIHOOD INFERENCE IN ROBUST LINEAR MIXED-EFFECTS MODELS USING MULTIVARIATE t DISTRIBUTIONS (2007, methodology): “For example Pinheiro and Bates (2000) have provided an nlme library in R/Splus for fitting non-linear random effects models. The robustness of the LMM based on t-distributions has been discussed by Pinheiro, Liu and Wu (2001). Clearly, this class of models extends the popular normal random effects m”
Conclusions beyond support: overconfident estimates in mixed models (2008, methodology): “The development of mixed-model methodology has proceeded rapidly over the past years (Snijders and Bosker 1999; Pinheiro and Bates 2000; Venables and Ripley 2002; Faraway 2006; Galwey 2006; Gelman and Hill 2007), and mixed models are now commonly used in analyses of observational and experimental da”
A simple test for random effects in regression models (2013, methodology): “Such models are discussed in detail in Pinheiro & Bates (2000), for example.”
Modelling Palaeoecological Time Series Using Generalised Additive Models (2018, background): “A continuous time first-order autoregressive process (CAR(1)) is a reasonable choice; it is the continuous-time equivalent of the first-order autoregressive process (AR(1)) and, simply stated, models the correlation between any two residuals as an exponentially decreasing function of h (φh), where h”
Forest Growth and Yield Modeling (2011, methodology): “To determine if a mixed model is necessary, the model should be fitted with and without random effects (Pinheiro and Bates, 2000).”
Adaptive management of biological systems: A review (2013, methodology): “We then used a generalized linear mixed model (GLMM; Pinheiro and Bates, 2000) from the nlme R package (Pinheiro et al., 2011) to compare ‘source’ articles against their paired ‘comparison’ article, using ‘article type’ (source or comparison) as a fixed effect.”
Comparison of Methods of Handling Missing Time-Invariant Covariates in Latent Growth Models Under the Assumption of Missing Completely at Random (2007, methodology): “The multilevel model (MLM) (Goldstein, 2003), also known as the hierarchical linear model (HLM) (Raudenbush & Bryk, 2002), and the mixedeffects model (Pinheiro & Bates, 2000) are clearly preferred statistical models for analyzing data spanning two or more levels.”
Restricted Likelihood Ratio Testing for Zero Variance Components in Linear Mixed Models (2008, background): “This behavior is especially pronounced in R lme, where the (restricted) log-likelihood is maximized with respect to the scaled logarithms of the variances (see Pinheiro and Bates 2000, sect.”
Use of within-array replicate spots for assessing differential expression in microarray experiments (2005, methodology): “On the other hand, iterative computational procedures are readily available to compute the numerical REML estimates σ̂g and ρ̂g for any given dataset (Pinheiro and Bates, 2000).”
Trade-offs between extraterritorial prospecting and helping in a cooperative mammal (2005, methodology): “Random terms allow the analysis to take account of repeated measures, and were included only if the analysis indicated significant repeatability at that level (as per Pinheiro & Bates 2000).”
Sexually distinct foraging strategies in an omnivorous seabird (2015, methodology): “Using linear mixed-effects models (Pinheiro and Bates 2000), we tested the effect of sex and breeding status on the duration of nest bouts, short trips, long trips, and on the foraging range of long trips.”
Rethinking the common garden in invasion research. (2009, methodology): “Analyses were conducted using mixed-effects models in R (function lmer, Pinheiro and Bates 2004).”